Artificial intelligence-aided rapid and accurate identification of clinical fungal infections by single-cell Raman spectroscopy.

Integrating artificial intelligence and new diagnostic platforms into routine clinical microbiology laboratory procedures has grown increasingly intriguing, holding promises of reducing turnaround time and cost and maximizing efficiency. At least one billion people are suffering from fungal infections, leading to over 1.6 million mortality every year. Despite the increasing demand for fungal diagnosis, current approaches suffer from manual bias, long cultivation time (from days to months), and low sensitivity (only 50% produce positive fungal cultures). Delayed and inaccurate treatments consequently lead to higher hospital costs, mobility and mortality rates. Here, we developed single-cell Raman spectroscopy and artificial intelligence to achieve rapid identification of infectious fungi. The classification between fungi and bacteria infections was initially achieved with 100% sensitivity and specificity using single-cell Raman spectra (SCRS). Then, we constructed a Raman dataset from clinical fungal isolates obtained from 94 patients, consisting of 115,129 SCRS. By training a classification model with an optimized clinical feedback loop, just 5 cells per patient (acquisition time 2 s per cell) made the most accurate classification. This protocol has achieved 100% accuracies for fungal identification at the species level. This protocol was transformed to assessing clinical samples of urinary tract infection, obtaining the correct diagnosis from raw sample-to-result within 1 h.

lncRNA ELFN1-AS1 enhances the progression of colon cancer by targeting miR-4270 to upregulate AURKB.

The oncogenic role of lncRNA ELFN1-AS1 has been described in different cancers, including colon cancer (CC). However, how ELFN1-AS1 regulates CC malignancy remains unclear. In this study, ELFN1-AS1, AURKB, and miR-4270 expression levels in CC cells and tissues were determined using RT-qPCR and western blotting. CCK-8 and wound healing assays were also performed to analyze alterations in CC cell proliferation and migration. The expression of apoptosis-related proteins (Bax and Bcl-2) was determined via western blot analysis. RNA immunoprecipitation (RIP) assays coupled with luciferase reporter assays were employed to verify the relationship between miR-4270, ELFN1-AS1, and AURKB. An in vivo assay was performed using xenograft tumors in mice to detect the change of tumor growth. It was found that AURKB and ELFN1-AS1 expression was upregulated, whereas miR-4270 was downregulated in CC cells and tissues. ELFN1-AS1 silencing exhibited anti-proliferative, anti-migratory, and pro-apoptotic effects in CC cells. The tumor-suppressive effect of ELFN1-AS1 silencing was verified using in vivo assays. MiR-4270 was predicted to be a target of ELFN1-AS1 and AURKB as a target of miR-4270. Their interactions were further elucidated using luciferase reporter and RNA RIP assays. More importantly, treatment with a miR-4270 inhibitor not only rescued the tumor-suppressing effect of ELFN1-AS1 silencing but also abrogated the tumor suppressor functions of AURKB silencing in CC cells. Taken together, the ELFN1-AS1/miR-4270/AURKB axis facilitates CC tumorigenesis; therefore, targeting this axis might be a promising intervention in preventing CC progression.

Farmland quality assessment using deep fully convolutional neural networks.

Farmland is the cornerstone of agriculture and is important for food security and social production. Farmland assessment is essential but traditional methods are usually expensive and slow. Deep learning methods have been developed and widely applied recently in image recognition, semantic understanding, and many other application domains. In this research, we used fully convolutional networks (FCN) as the deep learning model to evaluate farmland grades. Normalized difference vegetation index (NDVI) derived from Landsat images was used as the input data, and the China National Cultivated Land Grade Database within Jiangsu Province was used to train the model on cloud computing. We also applied an image segmentation method to improve the original results from the FCN and compared the results with classical machine learning (ML) methods. Our research found that the FCN can predict farmland grades with an overall F1 score (the harmonic mean of precision and recall) of 0.719 and F1 score of 0.909, 0.590, 0.740, 0.642, and 0.023 for non-farmland, level I, II, III, and IV farmland, respectively. Combining the FCN and image segmentation method can further improve prediction accuracy with results of fewer noise pixels and more realistic edges. Compared with conventional ML, at least in farmland evaluation, FCN provides better results with higher precision, recall, and F1 score. Our research indicates that by using remote sensing NDVI data, the deep learning method can provide acceptable farmland assessment without fieldwork and can be used as a novel supplement to traditional methods. The method used in this research will save a lot of time and cost compared with traditional means.

Mutation of a histidine-rich calcium-binding-protein gene in wheat confers resistance to Fusarium head blight.

Head or ear blight, mainly caused by Fusarium species, can devastate almost all staple cereal crops (particularly wheat), resulting in great economic loss and imposing health threats on both human beings and livestock1-3. However, achievement in breeding for highly resistant cultivars is still not satisfactory. Here, we isolated the major-effect wheat quantitative trait locus, Qfhs.njau-3B, which confers head blight resistance, and showed that it is the same as the previously designated Fhb1. Fhb1 results from a rare deletion involving the 3' exon of the histidine-rich calcium-binding-protein gene on chromosome 3BS. Both wheat and Arabidopsis transformed with the Fhb1 sequence showed enhanced resistance to Fusarium graminearum spread. The translation products of this gene's homologs among plants are well conserved and might be essential for plant growth and development. Fhb1 could be useful not only for curbing Fusarium head blight in grain crops but also for improving other plants vulnerable to Fusarium species.

A new lysosome-targetable fluorescent probe with a large Stokes shift for detection of endogenous hydrogen polysulfides in living cells.

Hydrogen polysulfides (H2Sn, n > 1) influence a variety of important biological functions and activities associated with hydrogen sulfide (H2S). The development of probes for rapid, selective, and sensitive detection of H2Sn still remains a great challenge. Lysosome plays crucial roles in various physiological processes among living cells, which arouse high interest in detecting endogenous lysosome-targetable H2Sn. To the best of our knowledge, there is no lysosome-targetable probe for H2Sn has been reported. In this work, a new lysosome-targetable probe NIPYNF, based on the scaffold of imidazo [1,5-]pyridine, with a large Stokes shift (215 nm), low detection limit (84 nM), fast response time (6 min) and low cytotoxicity was designed and synthesized. Furthermore, NIPYNF was successfully applied into the cell imaging for detection of endogenous lysosome-targetable H2Sn.

A high glycerol-containing leave-on scalp care treatment to improve dandruff.

Dandruff is a common cosmetic condition associated with flaky scalp skin and pruritus. It is generally treated with regular use of antifungal-based shampoos. Research into factors underlying the characteristic skin lesions has revealed perturbations in epidermal differentiation and a dramatic deterioration in the associated process of stratum corneum (SC) maturation. These observations suggest that directly addressing the quality of the SC could have a scalp benefit. In this study, the authors investigated the efficacy of a moisturising leave-on lotion (LOL) containing a high concentration of glycerol (10%) and other known skin benefit agents (saturated fatty acid and sunflower seed oil) to reduce dandruff over an 8-week treatment period with 3 applications per week. Results of expert visual grading and biophysical measurements of SC parameters (transepidermal water loss and hydration) revealed a significant reduction in the dandruffcondition over this period, with significant improvement in both SC water barrier function and hydration. These scalp skin benefits were maintained for up to a week following cessation of the treatment. This study indicates that use of a glycerol-rich substantive LOL, designed to directly improve the quality of the SC barrier can have a significant impact on the dandruff condition.

Serial expression of the truncated fragments of the nucleocapsid protein of CCHFV and identification of the epitope region.

The Crimean-congo hemorrhagic fever virus (CCHFV) is a geographically widespread fatal pathogen. Identification of the epitope regions of the virus is important for the diagnosis and epidemiological studies of CCHFV infections. In this study, expression vectors carrying series truncated fragments of the NP (nucleocapsid protein) gene from the S fragment of CCHFV strain YL04057 were constructed. The recombinant proteins were expressed in E.coli and purified for detection. The antigenic of the truncated fragments of NP was detected with a polyclonal serum (rabbit) and 2 monoclonal (mAbs) (14B7 and 43E5) against CCHFV by Western-blot analyses. The results showed that the three expressed constructs, which all contained the region 235AA to 305AA could be detected by mAbs polyclonal serum. The results suggest that region 235-305 aa of NP is a highly antigenic region and is highly conserved in the NP protein.

Monoclonal antibody induced with inactived EV71-Hn2 virus protects mice against lethal EV71-Hn2 virus infection.

BACKGROUND: Enterovirus 71 (EV71) is a viral pathogen that belongs to the Picornaviridae family, EV71-infected children can develop severe neurological complications leading to rapid clinical deterioration and death. RESULTS: In this study, several monoclonal antibodies (MAbs) were produced by immunizing mice with the inactived EV71 Henan (Hn2) virus strain. The isolated MAbs were characterised by in vitro neutralizing analysis and peptide ELISA. ELISA assay showed that the neutralizing monoclonal antibody 4E8 specifically reacted with synthetic peptides which contain amino acid 240-250 and 250-260 of EV71 VP1. The in vivo protection assay showed that 4E8 can protect two-day-old BALB/c mice against the lethal challenge of EV71 virus. CONCLUSION: The MAb 4E8 could be a promising candidate to be humanized and used for treatment of EV71 infection.

Sequence analysis of six enterovirus 71 strains with different virulences in humans.

Enterovirus 71 (EV71) infection is the main cause of hand, foot and mouth disease (HFMD) and has been associated with severe neurological diseases resulting in high mortalities. In this study, six EV71 strains isolated from patients with different clinical symptoms were sequenced and analyzed in a mouse model of EV71 infection. In a phylogenetic tree, based on the complete VP1 gene sequence, all six strains grouped into the C4 genotype. The sequence analysis revealed that there are nucleotide changes clustered in the internal ribosome entry site (IRES) element of the 5'-nontranslated region (5'-NTR), as well as amino acid differences clustered in the non-structural proteins. Importantly, we identified a unique amino acid difference (Val(1994)-Ile(1994)) that distinguished the more virulent strains, Anhui1 (Ah1), Henan1 (Hn1) and Henan2 (Hn2) from the less virulent strains, Chongqing1 (Cq1), Chongqing2 (Cq2) and Chongqing3 (Cq3). This amino acid difference is located in the finger domain of the viral RNA-dependent RNA polymerase 3D (3D(pol)). Furthermore, two-day-old Balb/c mice were inoculated with the Ah1, Hn1, Hn2, Cq1, Cq2 and Cq3 isolates by the intracerebral or intraperitoneal routes. All of the mice inoculated with Ah1, Hn1 and Hn2 isolates developed hind-leg paralysis and subsequently died. Mice inoculated with the Cq1, Cq2 or Cq3 isolates survived throughout the 21-day observation period. These results show that clinical isolates of EV71 associated with disease of different severity in humans have characteristic sequence differences and cause different mortality rates when inoculated into mice. These data also provide a rational basis to investigate the molecular determinants of EV71 pathogenesis using a reverse genetic approach.

Ginkgo biloba extract alleviates liver fibrosis induced by CCl in rats.

AIMS: To investigate the protective effect of Ginkgo biloba extract (GbE) on liver fibrosis induced by carbon tetrachloride (CCl4) in rats and expressions of transforming growth factor beta1 (TGF-beta1) and collagen I during this period. METHODS: The effect of GbE on liver fibrogenesis was detected by hematoxylin and eosin staining (H&E staining), Masson's trichrome staining, and electron microscope study. Blood samples were collected for measurement of alanine aminotransferase (ALT), aspartate aminotransferase (AST) and albumin. Malondialdehyde (MDA) in liver tissue was detected by the thiobarbituric acid (TBA) method. Immunohistochemistry assay and RT-PCR were used to examine the protein expressions and mRNA levels of TGF-beta1 and collagen I, respectively. RESULTS: H&E, Masson's trichrome stainings and electron microscope study showed liver fibrosis in rats was greatly alleviated when treated with GbE. Additionally, there was a remarkable improvement of serum ALT, AST, albumin and MDA in the GbE-treated group. Immunohistochemistry and RT-PCR results showed GbE intervention significantly inhibited TGF-beta1 and collagen I expressions in rat liver. No side effects of GbE were found during these experiments. But GbE could not reverse the pathological changes of liver fibrosis completely when compared with normal control. CONCLUSION: GbE can partially protect rat liver from the fibrogenesis induced by CCl4. The mechanism may lie in its effect of inhibiting oxidative stress caused by liver injury and expressions of signal molecules such as TGF-beta1. GbE may thus be of potential help as a medicament or food additive for alleviation of liver fibrogenesis.

Effect of ginkgo biloba extract on livers in aged rats.

AIM: To investigate the protective effect of ginkgo biloba extract (GBE) on livers of aged rats and the associated mechanisms. METHODS: Two-mo- and 20-mo-old rats were treated with GBE/saline for 3 mo. Liver tissue samples from 5-mo-old rats treated with saline (group Y) and 23-mo-old rats treated with GBE (group E) or saline (group N) were used for histopathological examinations (hematoxylin-eosin and Masson staining, Lipofuscin staining-Schmorl staining) and determination of expression of tissue inhibitor-1 of metalloproteinase (TIMP-1) and the level of malondialdehyde (MDA), glutathione peroxidase (GPx) and superoxide dismutase (SOD). Blood samples were collected for determination of alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (TBIL) and albumin. RESULTS: Microscopic studies with Masson staining revealed mild liver fibrosis in aged rats (group N), while the livers of aged rats receiving GBE (group E) showed amelioration in fibrosis (2.2+/-0.1 vs 2.8+/-0.1, P<0.01) and deposition of lipofuscin (33.7+/-5.3 vs 62.8+/-5.7, P<0.01). The expression of TIMP-1 and the level of liver MDA (1.0+/-0.1 vs 1.2+/-0.2, P<0.05) also decreased but the activity of GPx (97.1+/-15.3 vs 61.8+/-14.5, P<0.01) increased in group E. Compared with group Y, the level of liver MDA (0.8+/-0.1 vs 1.2+/-0.2, P<0.01), lipofuscin (32.4+/-6.0 vs 62.8+/-5.7, P<0.01) and TIMP-1 expression were increased, while the activity of GPx (103.2+/-17.6 vs 61.8+/-14.5, P<0.01) and SOD (16.7+/-4.4 vs 11.8+/-3.9, P<0.05) was decreased in group N. There was no difference in liver function among these three groups. CONCLUSION: GBE has protective effects on aging liver. The possible mechanisms might be its antioxidant activity and inhibition of TIMP-1 expression.

Ginkgo biloba extract reverses CCl4-induced liver fibrosis in rats.

AIM: To study the reversing effect of Ginkgo biloba extract (GbE) on established liver fibrosis in rats. METHODS: Following confirmation of CCl(4)-induced liver fibrosis, GbE or saline was administrated to the rats for 4 weeks. The remaining rats received neither CCl(4) nor GbE as normal control. The four groups were compared in terms of serum enzymes, tissue damage, expression of alphaSMA and tissue inhibitor-1 of metalloproteinase (TIMP-1) and metalloproteinase-1 (MMP-1). RESULTS: Compared with saline-treated group, liver fibrosis rats treated with GbE had decreased serum total bilirubin (P<0.01) and aminotransferase levels (P<0.01) and increased levels of serum albumin (P<0.01). Microscopic studies revealed that the livers of rats receiving GbE showed alleviation in fibrosis (P<0.05) as well as expression of alphaSMA (P<0.01). The liver collagen and reticulum contents were lower in rats treated with GbE than saline-treated group (P<0.01). RT-PCR revealed that the level of TIMP-1 decreased while the level of MMP-1 increased in GbE group. CONCLUSION: Administration of GbE improved CCl(4)-induced liver fibrosis. It is possibly attributed to its effect of inhibiting the expression of TIMP-1 and promoting the apoptosis of hepatic stellate cells.

[Potential molecular mechanism of multiple organ dysfunction syndrome induced by hemorrhage and endotoxin].

OBJECTIVE: To investigate the possible molecular mechanism of multiple organ dysfunction syndrome (MODS) associated with hemorrhagic shock followed by resuscitation and endotoxin. METHODS: A rabbit model of MODS after hemorrhagic shock followed by resuscitation and endotoxin was used in this study. The expression of I-kappaB kinase-beta (IKK-beta), the activity of nuclear factor-kappaB (NF-kappaB) in macrophage (PAM) and Kupffer cell (KC), the concentration of tumor necrosis factor-alpha (TNF-alpha) in the culture supernatant were measured by in situ hybridization (ISH), electrophoretic mobility shift assay (EMSA) and enzyme linked immunoadsorbent assay (ELISA), respectively. Then the blood gas, biochemistrical and pathological changes in lungs, liver and intestines were examined in each groups. RESULTS: In the MODS group, the expression of IKK-beta mRNA (0.15+/-0.03, 0.17+/-0.04), the activity of NF-kappaB (1.49+/-0.30, 1.72+/-0.36) and the levels of TNF-alpha[(279.74+/-25.91)ng/L, (300.05+/-30.86)ng/L] in PAM and KCs were significantly higher than those of normal controls[IKK-beta mRNA 0.03+/-0.01 and 0.02+/-0.01; NF-kappaB 0.25+/-0.06 and 0.31+/-0.10, TNF-alpha (137.33+/-6.09)ng/L and (134.85+/-12.09)ng/L, respectively, all P<0.01]. Also, the contents of blood urea nitrogen (BUN), alanine aminotransferase (ALT) in plasma significantly increased, the arterial oxygen partial pressure decreased, and the severity of organ damages in lungs, liver as well as intestines increased following MODS. CONCLUSION: The IKK-beta expression, NF-kappaB activation and cytokine release may play important roles in the pathogenesis of acute lung injury and MODS.

[Effects of polymixin B on I-kappaB kinase mRNA expression in lipopolysaccharide- induced pulmonary alveolar macrophages].

OBJECTIVE: To investigate effects of polymixin B (PMB) on I-kappaB kinase(IKK-beta), inhibitor protein(IkappaB-alpha) and nuclear factor-kappa B(NF-kappaB) in lipopolysaccharide(LPS)-induced pulmonary alveolar macrophages (PAM), and explore the anti-inflammatory mechanism of PMB. METHODS: PAM from rats collected by bronchoalveolar lavage was cultured and divided into three groups. In the control group, PAM was not stimulated with LPS and not treated with PMB. In the LPS stimulated group, PAM was stimulated with LPS. In the PMB treated group, PAM was pretreated with PMB half an hour prior to LPS stimulation. The expression of IKK-beta mRNA, level of IkappaB-alpha and the activity of NF-kappaB in PAM were measured by in situ hybridization(ISH), enzyme linked immunoadsorbent assay (ELISA) and electrophoretic mobility shift assay(EMSA), respectively. RESULTS: In the LPS stimulated group, the expression of IKK-beta mRNA (0.147+/-0.015) and activity of NF-kappaB (0.828+/-0.019) in PAM significantly increased, whereas levels of IkappaB-alpha (0.228+/-0.021) decreased (all P<0.01) in PMB treated groups. The expression of IKK-beta mRNA (0.112+/-0.022) and activity of NF-kappaB (0.358+/-0.011) were down-regulated while level of IkappaB-alpha (0.477+/-0.016) was up-regulated(P<0.01). CONCLUSION: LPS might induce expression of IKK-beta mRNA, degradation of IkappaB-alpha and activation of NF-kappaB PMB could inhibit the expression of IKK-beta, degradation of IkappaB-alpha and activation of NF-kappaB, showing marked anti-inflammatory property.